jolly-roger 0.0.2__tar.gz

jolly_roger-0.0.2/.copier-answers.yml

@@ -0,0 +1,12 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 2025.05.02-13-g4bc2312
+_src_path: gh:scientific-python/cookie
+backend: hatch
+email: alec.thomson@csiro.au
+full_name: Alec Thomson
+license: BSD
+org: flint-crew
+project_name: jolly-roger
+project_short_description: The pirate flagger
+url: https://github.com/flint-crew/jolly-roger
+vcs: true

jolly_roger-0.0.2/.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

jolly_roger-0.0.2/.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

jolly_roger-0.0.2/.github/CONTRIBUTING.md

@@ -0,0 +1,77 @@
+See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
+description of best practices for developing scientific packages.
+
+[spc-dev-intro]: https://learn.scientific-python.org/development/
+
+# Quick development
+
+The fastest way to start with development is to use nox. If you don't have nox,
+you can use `uvx nox` to run it without installing, or `uv tool install nox`. If
+you don't have uv, you can
+[install it a variety of ways](https://docs.astral.sh/uv/getting-started/installation/),
+including with pip, pipx, brew, and just downloading the binary (single file).
+
+To use, run `nox`. This will lint and test using every installed version of
+Python on your system, skipping ones that are not installed. You can also run
+specific jobs:
+
+```console
+$ nox -s lint  # Lint only
+$ nox -s tests  # Python tests
+$ nox -s docs  # Build and serve the docs
+$ nox -s build  # Make an SDist and wheel
+```
+
+Nox handles everything for you, including setting up an temporary virtual
+environment for each run.
+
+# Setting up a development environment manually
+
+You can set up a development environment by running:
+
+```bash
+uv sync
+```
+
+# Pre-commit
+
+You should prepare pre-commit, which will help you by checking that commits pass
+required checks:
+
+```bash
+uv tool install pre-commit # or brew install pre-commit on macOS
+pre-commit install # Will install a pre-commit hook into the git repo
+```
+
+You can also/alternatively run `pre-commit run` (changes only) or
+`pre-commit run --all-files` to check even without installing the hook.
+
+# Testing
+
+Use pytest to run the unit checks:
+
+```bash
+uv run pytest
+```
+
+# Coverage
+
+Use pytest-cov to generate coverage reports:
+
+```bash
+uv run pytest --cov=jolly-roger
+```
+
+# Building docs
+
+You can build and serve the docs using:
+
+```bash
+nox -s docs
+```
+
+You can build the docs only with:
+
+```bash
+nox -s docs --non-interactive
+```

jolly_roger-0.0.2/.github/actions/setup-deps/action.yml

@@ -0,0 +1,9 @@
+name: "Setup Dependencies"
+description: "Install deps"
+runs:
+  using: "composite"
+  steps:
+    - name: Install casacore and boost
+      shell: bash
+      run: |
+        sudo apt install -y build-essential libcfitsio-dev liblapack-dev libboost-python-dev python3-dev wcslib-dev casacore-dev

jolly_roger-0.0.2/.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

jolly_roger-0.0.2/.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

jolly_roger-0.0.2/.github/workflows/cd.yml

@@ -0,0 +1,56 @@
+name: CD
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  publish:
+    needs: [dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
+      attestations: write
+      contents: read
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - name: Generate artifact attestation for sdist and wheel
+        uses: actions/attest-build-provenance@v2
+        with:
+          subject-path: "dist/*"
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

jolly_roger-0.0.2/.github/workflows/ci.yml

@@ -0,0 +1,76 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - uses: astral-sh/setup-uv@v6
+
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --hook-stage manual --all-files
+
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    needs: [pre-commit]
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+        runs-on: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v6
+      - uses: actions/cache@v4
+        id: cache-uv
+        with:
+          path: ~/.cache/uv
+          key: ${{ runner.os }}-python-${{ matrix.python-version }}-uv
+      - name: Install dependencies
+        uses: ./.github/actions/setup-deps
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install package
+        run: uv sync
+
+      - name: Test package
+        run: >-
+          uv run pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v5.4.3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

jolly_roger-0.0.2/.gitignore

@@ -0,0 +1,158 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# setuptools_scm
+jolly_roger/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp

jolly_roger-0.0.2/.pre-commit-config.yaml

@@ -0,0 +1,84 @@
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+exclude: ^.cruft.json|.copier-answers.yml$
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.19.1"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v5.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.11.13"
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.16.0"
+    hooks:
+      - id: mypy
+        files: jolly_roger|tests
+        args: ["--ignore-missing-imports"]
+        additional_dependencies:
+          - pytest
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.4.1"
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli; python_version<'3.11'
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.24.1"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.33.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs

jolly_roger-0.0.2/.readthedocs.yaml

@@ -0,0 +1,16 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.13"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv sync --group docs
+    - uv run python -m sphinx -T -b html -d docs/_build/doctrees -D language=en
+      docs $READTHEDOCS_OUTPUT/html

jolly_roger-0.0.2/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, Alec Thomson.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the vector package developers nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

jolly_roger-0.0.2/PKG-INFO

@@ -0,0 +1,87 @@
+Metadata-Version: 2.4
+Name: jolly-roger
+Version: 0.0.2
+Summary: The pirate flagger
+Project-URL: Homepage, https://github.com/flint-crew/jolly-roger
+Project-URL: Bug Tracker, https://github.com/flint-crew/jolly-roger/issues
+Project-URL: Discussions, https://github.com/flint-crew/jolly-roger/discussions
+Project-URL: Changelog, https://github.com/flint-crew/jolly-roger/releases
+Author-email: Alec Thomson <alec.thomson@csiro.au>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 1 - Planning
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: astropy
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: python-casacore>=3.6.0
+Requires-Dist: tqdm
+Description-Content-Type: text/markdown
+
+# jolly-roger
+
+[![Actions Status][actions-badge]][actions-link]
+[![Documentation Status][rtd-badge]][rtd-link]
+
+[![PyPI version][pypi-version]][pypi-link]
+<!-- [![Conda-Forge][conda-badge]][conda-link] -->
+[![PyPI platforms][pypi-platforms]][pypi-link]
+
+<!-- [![GitHub Discussion][github-discussions-badge]][github-discussions-link] -->
+
+<!-- SPHINX-START -->
+
+<!-- prettier-ignore-start -->
+[actions-badge]:            https://github.com/flint-crew/jolly-roger/workflows/CI/badge.svg
+[actions-link]:             https://github.com/flint-crew/jolly-roger/actions
+[conda-badge]:              https://img.shields.io/conda/vn/conda-forge/jolly-roger
+[conda-link]:               https://github.com/conda-forge/jolly-roger-feedstock
+[github-discussions-badge]: https://img.shields.io/static/v1?label=Discussions&message=Ask&color=blue&logo=github
+[github-discussions-link]:  https://github.com/flint-crew/jolly-roger/discussions
+[pypi-link]:                https://pypi.org/project/jolly-roger/
+[pypi-platforms]:           https://img.shields.io/pypi/pyversions/jolly-roger
+[pypi-version]:             https://img.shields.io/pypi/v/jolly-roger
+[rtd-badge]:                https://readthedocs.org/projects/jolly-roger/badge/?version=latest
+[rtd-link]:                 https://jolly-roger.readthedocs.io/en/latest/?badge=latest
+
+<!-- prettier-ignore-end -->
+
+The pirate flagger!
+
+# Installation
+
+`pip install jolly-roger`
+
+# About
+
+This package attempts to flag visibilities that are contaminated by the Sun and uses a fairly simple heuristic based on the geometry of an interferometer.
+
+In short, `jolly_roger` flags based on the projected baseline length should the array be tracking the Sun. The projected baseline length between some phased direction being tracked and the Sun can be significantly different. `jolly_roger` attempts to leverage this by only flagging data where the projected baseline length is between some nominal range that corresponds to angular scales associated with the Sun.
+
+`jolly_roger` makes no guarentess about removing all contaminated visibilities, nor does it attempt to peel/subtract the Sun from the visibility data.
+
+## How does it work?
+
+`jolly_roger` will recompute the (u,v,w)-coordinates of a measurement set as if it were tracking the Sun, from which (u,v)-distances are derieved for each baseline and timestep. An updated `FLAG` column can then be inserted into the measurement set suppressing visibilities that would be sensitive to a nominated range of angular scales.
+
+## Example
+
+`jolly_roger` has a CLI entry point that can be called as:
+
+```
+jolly_flagger scienceData.EMU_1141-55.SB47138.EMU_1141-55.beam00_averaged_cal.leakage.ms --min-horizon-limit-deg '-2' --max-horizon-limit-deg 30 --min-scale-deg 0.075
+```
+
+Here we are flagging visibilities that correspond to instances where:
+- the Sun has an elevation between -2 and 30 degrees, and
+- they are sensitive to angular scales between 0.075 and 1.0 segrees.

jolly_roger-0.0.2/README.md

@@ -0,0 +1,57 @@
+# jolly-roger
+
+[![Actions Status][actions-badge]][actions-link]
+[![Documentation Status][rtd-badge]][rtd-link]
+
+[![PyPI version][pypi-version]][pypi-link]
+<!-- [![Conda-Forge][conda-badge]][conda-link] -->
+[![PyPI platforms][pypi-platforms]][pypi-link]
+
+<!-- [![GitHub Discussion][github-discussions-badge]][github-discussions-link] -->
+
+<!-- SPHINX-START -->
+
+<!-- prettier-ignore-start -->
+[actions-badge]:            https://github.com/flint-crew/jolly-roger/workflows/CI/badge.svg
+[actions-link]:             https://github.com/flint-crew/jolly-roger/actions
+[conda-badge]:              https://img.shields.io/conda/vn/conda-forge/jolly-roger
+[conda-link]:               https://github.com/conda-forge/jolly-roger-feedstock
+[github-discussions-badge]: https://img.shields.io/static/v1?label=Discussions&message=Ask&color=blue&logo=github
+[github-discussions-link]:  https://github.com/flint-crew/jolly-roger/discussions
+[pypi-link]:                https://pypi.org/project/jolly-roger/
+[pypi-platforms]:           https://img.shields.io/pypi/pyversions/jolly-roger
+[pypi-version]:             https://img.shields.io/pypi/v/jolly-roger
+[rtd-badge]:                https://readthedocs.org/projects/jolly-roger/badge/?version=latest
+[rtd-link]:                 https://jolly-roger.readthedocs.io/en/latest/?badge=latest
+
+<!-- prettier-ignore-end -->
+
+The pirate flagger!
+
+# Installation
+
+`pip install jolly-roger`
+
+# About
+
+This package attempts to flag visibilities that are contaminated by the Sun and uses a fairly simple heuristic based on the geometry of an interferometer.
+
+In short, `jolly_roger` flags based on the projected baseline length should the array be tracking the Sun. The projected baseline length between some phased direction being tracked and the Sun can be significantly different. `jolly_roger` attempts to leverage this by only flagging data where the projected baseline length is between some nominal range that corresponds to angular scales associated with the Sun.
+
+`jolly_roger` makes no guarentess about removing all contaminated visibilities, nor does it attempt to peel/subtract the Sun from the visibility data.
+
+## How does it work?
+
+`jolly_roger` will recompute the (u,v,w)-coordinates of a measurement set as if it were tracking the Sun, from which (u,v)-distances are derieved for each baseline and timestep. An updated `FLAG` column can then be inserted into the measurement set suppressing visibilities that would be sensitive to a nominated range of angular scales.
+
+## Example
+
+`jolly_roger` has a CLI entry point that can be called as:
+
+```
+jolly_flagger scienceData.EMU_1141-55.SB47138.EMU_1141-55.beam00_averaged_cal.leakage.ms --min-horizon-limit-deg '-2' --max-horizon-limit-deg 30 --min-scale-deg 0.075
+```
+
+Here we are flagging visibilities that correspond to instances where:
+- the Sun has an elevation between -2 and 30 degrees, and
+- they are sensitive to angular scales between 0.075 and 1.0 segrees.